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We describe a new class of DNA-like oligomers made exclusively of nonnatural, stable C-nucleosides. The nucleosides comprise four types of nonnatural bases attached to a deoxyribose through an acetylene bond with the β-configuration. The artificial DNA forms right-handed duplexes and triplexes with the complementary artificial DNA. The hybridization occurs spontaneously and sequence-selectively, and the resulting duplexes have thermal stabilities very close to those of natural duplexes. The artificial DNA might be applied to a future extracellular genetic system with information storage and amplifiable abilities.

This paper was first submitted in February, but I hadn't heard about it until now. Absolutely incredible. Even more so that this should occur in the same year as the Memristor's physical inception.

Fleshing out for Mods (please don't hurt me Elki! ) :

What are the implications of this do you think, in terms of humanity beginning to steer the course of it's own evolution. One far-reaching possibility of this is the direct encoding of data into newly-created organisms, and also lifeforms with triple helix DNA. Does mankind have the right to be doing this?

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I don't think it's any different than synthesizing medicines or anything else. Of course, I'm worried what can come out of this, but I'd also be interested in seeing the possibilities. I don't see why not.

bowen on July 2008

Warning: I am a programmer/sysop. Do not take my word as law in any other fields, it is not professional advice.

I think its cool and we have every right to tinker with DNA, artificial or natural.

And practical use is engineering business. Scientists don't worry about such trivial things, since, you know, funding is endless!

I'm sure some clever people have some big ideas or they wouldn't be doing the research. The technology and processes developed to do things like this might end up being more useful then anything they create in the short term.

What are the implications of this do you think, in terms of humanity beginning to steer the course of it's own evolution. One far-reaching possibility of this is the direct encoding of data into newly-created organisms, and also lifeforms with triple helix DNA. Does mankind have the right to be doing this?

Its not particularly relevant to steering our own genomic evolution unless you plan on building a new human-like thing from the ground up using these artificial nucleotides, and the amount of work going into replicating all the stuff DNA does (which we are a long way from understanding currently) would be enormous. Engineered bacteria in our system would be pretty sweet though.

@ElJeffe, triple code allows greater redundancy of information and scope for error checking, theoretically enabling mutation/radiation resistant designs of organisms and longer term molecular information storage. However make current cellular machinery work on triplicate strands is again a task of enormous complexity, especially as we don't know what everything does yet.

@ElJeffe, triple code allows greater redundancy of information and scope for error checking, theoretically enabling mutation/radiation resistant designs of organisms and longer term molecular information storage. However make current cellular machinery work on triplicate strands is again a task of enormous complexity, especially as we don't know what everything does yet.

So in theory, organisms with triple-strand DNA would evolve more slowly than regular critters?

ElJeffe on July 2008

Maddie: "I named my feet. The left one is flip and the right one is flop. Oh, and also I named my flip-flops."

@ElJeffe, triple code allows greater redundancy of information and scope for error checking, theoretically enabling mutation/radiation resistant designs of organisms and longer term molecular information storage. However make current cellular machinery work on triplicate strands is again a task of enormous complexity, especially as we don't know what everything does yet.

So in theory, organisms with triple-strand DNA would evolve more slowly than regular critters?

Depending on their DNA repair ability they could have less genomic change per unit time, 'evolve' not really being relevant here. Its like a [fast make of car Dis knows nothing about] verses [slower make Dis knows nothing about], sure it could go faster/suffer less genetic drift, but it doesn't have to.

Naturally with your engineered organism(TM) you want it as unchanging as possible, and triple helix would theoretically allow more stability to be engineered in (as each newly synthesized strand could be checked by the cellular machinery against two other strands rather than just the current one), hence the glee over the development.

What are the implications of this do you think, in terms of humanity beginning to steer the course of it's own evolution. One far-reaching possibility of this is the direct encoding of data into newly-created organisms, and also lifeforms with triple helix DNA. Does mankind have the right to be doing this?

There are myriad implications that could be derived from being able to control the very building blocks of life. You can say that it might be exploited and offered to only the rich and powerful, either in secrecy or due to cost. One might also say that this will drastically improve the quality of life for everyone over the next 20 years. This could also be used as a weapon to commit genocide on a grand scale. That's just to name a few.

As for do we have the right? In my eyes, absolutely. Why should we be bound by ridiculously stupid diseases and suffering for those ailments? Why the hell wouldn't we?

I -think- there's a distinction to be made here between environmental mutations and reproductive mutations.

Triple-stranded DNA (tsDNA) organisms could be radiation resistant, as well as resistant to to other forms of environmental mutation. With double-stranded DNA (dsDNA), if one base gets screwed up, your DNA correction machinery doesn't know which of the two bases is the correct one. With tsDNA, presumably one base would not match the other two and could be identified as incorrect. (Though how you have complementary 3-base matching with 4 nucleotides is beyond me...)

As for reproductive mutations, which is I think is typically what we consider to be the driving force behind genetic variety, which in turn is a critical element in evolution via natural selection, I don't know that tsDNA is any more mutation-resistant. If it would replicate the same way our dsDNA does, then the three strands would split and two additional strands would be created to bind to each. That would make it just as likely to commit errors I think, maybe even more given that simply more bases would be required. Unless the argument is that three-way complementation makes breaking that complementation energetically unfeasible, but I don't know if that'd really hold up in practice, given the many base-analagous molecules we know exist (Uracil anyone?). That'd mean tsDNA organisms could "evolve" just as easily, just be radiation-resistant.

Dis suggested that "each newly synthesized strand could be checked by the cellular machinery against two other strands rather than just the current one" but I'm not really sure how that'd work. So an organism with strands ABC ejects strand C, replicates strand c off strands AB, then ejects strand B, binds B with C, writes strands b off strands Ac, then ejects A, binds A back with BC, and writes strand a off strands bc, creating ABC/abc? That seems pretty convoluted, but hell, it's not like molecular biology isn't ridiculously convoluted already.

Of course, this is all just hypothetical off the top of my head. What -isn't- hypothetical is that quadruple-stranded DNA results in super mutants.

I don't see why triple-stranded DNA would for some reason be more stable then double stranded DNA. I mean, these aren't covalent bonds and that's a hell of a lot more steric hindrance in there. As I understand it under the right conditions regular DNA will anneal to form a triple stranded structure, but the fact we never see it to the point of not worrying about it suggests that yes, it's probably quite unstable. Subbing in a few differenty bases doesn't get you out of that conumdrum.

The other point is, there is currently no cell replication machinery in existence which deals with triple stranded DNA. Engineering such a thing would be - make no mistake - a huge technical undertaking.

Finally, there's also no conceivable error checking system for DNA that can't be implemented more efficiently as a variation of single stranded DNA, if only because it would be modifying a largely functional system with many many layers of redundancy and error checking already. And, chances are whatever you can think of, some variant is already partially or wholly implemented by evolution.

im fine with people doing it, because by the time they get it to the point where it actually works (let alone we figure out the side effects) ill probably be dead and gone. im not in the nature of saving people from their own stupidity.

How much of this stuff can be retrofitted into an already existing organism? Doesn't your body have to be born with these new designs from the start?

Absolutely none of it. A tsDNA organism would need its own DNA protein machinery, and we have no idea how to produce any of it. We don't even know how dsDNA organisms (ie, us) acquired their DNA protein machinery.

How much of this stuff can be retrofitted into an already existing organism? Doesn't your body have to be born with these new designs from the start?

Absolutely none of it. A tsDNA organism would need its own DNA protein machinery, and we have no idea how to produce any of it. We don't even know how dsDNA organisms (ie, us) acquired their DNA protein machinery.

What's the current theory on that? I remember one fucking-crazy genetics teacher telling us it had something to do with virii and everyone thought he was fucking-crazy. Did I mention he was fucking-crazy?

bowen on July 2008

Warning: I am a programmer/sysop. Do not take my word as law in any other fields, it is not professional advice.

I'm trying to gently insist that the triplex is not the most interesting thing about this discovery. Actually, most of the biological ideas people have are not the most interesting thing either - something like this is actually far more relevant in my Ph D project where I'm using DNA as a structural element to link nanoparticles. Something which is entirely dissimilar to normal DNA bases means the potential to engineer things which are resistant to biological conditions.

DNA which doesn't react to any of the normal DNA-handling proteins would be just spectacular.

How much of this stuff can be retrofitted into an already existing organism? Doesn't your body have to be born with these new designs from the start?

Absolutely none of it. A tsDNA organism would need its own DNA protein machinery, and we have no idea how to produce any of it. We don't even know how dsDNA organisms (ie, us) acquired their DNA protein machinery.

What's the current theory on that? I remember one fucking-crazy genetics teacher telling us it had something to do with virii and everyone thought he was fucking-crazy. Did I mention he was fucking-crazy?

How much of this stuff can be retrofitted into an already existing organism? Doesn't your body have to be born with these new designs from the start?

Absolutely none of it. A tsDNA organism would need its own DNA protein machinery, and we have no idea how to produce any of it. We don't even know how dsDNA organisms (ie, us) acquired their DNA protein machinery.

What's the current theory on that? I remember one fucking-crazy genetics teacher telling us it had something to do with virii and everyone thought he was fucking-crazy. Did I mention he was fucking-crazy?

He was probably talking about viral RNA.

No, someone asked him what he's heard about the origination of the structures in which DNA can replicate itself and form new DNA and how it might have started the first life. I hated that class, and he hated it too.

bowen on July 2008

Warning: I am a programmer/sysop. Do not take my word as law in any other fields, it is not professional advice.

No, someone asked him what he's heard about the origination of the structures in which DNA can replicate itself and form new DNA and how it might have started the first life. I hated that class, and he hated it too.

What he's heard? I'd have assumed a genetics teacher would have had some idea - anyway the teacher was possibly referring to this hypothesis.

@electricitylikesme: but wouldn't triplex DNA be even more resistant to enzymatic action? Also as a point of interest would the artificial DNA used in engineering require repair mechanisms to alleviate the molecular damage (free radicals et al) regular DNA needs to be checked for all the time?

Actually, he might have been talking about a nice little paper by Patrick Forterre. It is not completely crazy, but let's just say it does not explain that much either. Read about here:http://www.ncbi.nlm.nih.gov/pubmed/16505372?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum
In short, his paper states that viruses (virii never refers to biological viruses, only the computer kind) might have been instrumental in the transition from a RNA world to the present DNA world. Three viruses would have taken over a RNA organism each and given rise to bacteria, archaea and eukarytes. I remember reading this paper when it came out, and yeah, it is pretty out there. However, Forterre is highly respected and the paper is certainly worth a read.

Yeah that looks about right. Is this the mainstream theory or is there a different one now?

Kinda, its a 'leading' hypothesis about a stage of abiogenesis at least, the abiogenesis wiki seems like an okay page if you want an overview.

RNA world doesn't really have anything to do with viruses though.

Edit: re. the above post, I'm pretty sure the accepted explanation for the relationship between the three domains is going to be lateral gene transfer resulting in a ring of life at the base of the tree of life. A lot of phylogenetic analyses are coming up with encouraging results for this hypothesis, and increasingly phylogenomic analyses are pointing to it as well. That is not to say that the hypothesis in the linked article is wrong, but rather that the ambiguity in the origins of the three domains is likely not evidence towards a viral transition from RNA to DNA. A simpler explanation would be that the RNA to DNA transition occurred once (as far as we're concerned) and then continued divergent evolution, with lateral gene transfers, resulted in the three domains.

Whether tsDNA would be more resistant to enzymatic action's something of a moot question. It would depend on the enzymes that could facilitate such actions, and since none of those exist, how could we possibly know? As a natural mode of existence, tsDNA seems absurd, since it would be far less likely to spontaneously arise, would require more complex enzymatic actions, and data redundancy isn't useful on an evolutionary scale. So it depends on whether we're talking about tsDNA organisms, or tsDNA data encoding, but really both are really far off, considering we're still working on ways to better sequence dsDNA.

Yeah that looks about right. Is this the mainstream theory or is there a different one now?

Kinda, its a 'leading' hypothesis about a stage of abiogenesis at least, the abiogenesis wiki seems like an okay page if you want an overview.

RNA world doesn't really have anything to do with viruses though.

Whether tsDNA would be more resistant to enzymatic action's something of a moot question. It would depend on the enzymes that could facilitate such actions, and since none of those exist, how could we possibly know? As a natural mode of existence, tsDNA seems absurd, since it would be far less likely to spontaneously arise, would require more complex enzymatic actions, and data redundancy isn't useful on an evolutionary scale. So it depends on whether we're talking about tsDNA organisms, or tsDNA data encoding, but really both are really far off, considering we're still working on ways to better sequence dsDNA.

Of course it has nothing to do with Viruses, except that's what a good portion of them basically are just RNA units. I was just asking if my genetics teacher knew what he was off about, that RNA-viruses lead to the arrival of DNA cells and structures.

bowen on July 2008

Warning: I am a programmer/sysop. Do not take my word as law in any other fields, it is not professional advice.

This is getting of-topic, but when you are refering to the "Ring of life" are you talking about Riveras and Lakes paper? There has been quite a bit of controversy over that one. And I would not say that there is any accepted theory about how the three domains arose. Sure, it is more parsimonous to assume that the transition from RNA to DNA only happened once, and that eukaryotes are the result of some sort of genome fusion, singular or at multiple steps, is fairly clear. However, any theories that goes further than that are unproven to say the least.... but that is just my personal opinion of course. A good/bad thing with working in this field is that the data is so inconclusive that it is very hard to prove anyone wrong, which is why I feel that especially the established scientist that come up with theories like these ones should be carefull since findings published in high-impact journals can tend to become generally established "truths" even though they are actually resting on weak support. Anyway, enough with the ranting.

bowen:

Your teacher was probably not that crazy, assuming he was talking about Forterres theory. However, it is not something I would talk about if i did not want to confuse my students....

This is getting of-topic, but when you are refering to the "Ring of life" are you talking about Riveras and Lakes paper? There has been quite a bit of controversy over that one. And I would not say that there is any accepted theory about how the three domains arose. Sure, it is more parsimonous to assume that the transition from RNA to DNA only happened once, and that eukaryotes are the result of some sort of genome fusion, singular or at multiple steps, is fairly clear. However, any theories that goes further than that are unproven to say the least.... but that is just my personal opinion of course. A good/bad thing with working in this field is that the data is so inconclusive that it is very hard to prove anyone wrong, which is why I feel that especially the established scientist that come up with theories like these ones should be carefull since findings published in high-impact journals can tend to become generally established "truths" even though they are actually resting on weak support. Anyway, enough with the ranting.

bowen:

Your teacher was probably not that crazy, assuming he was talking about Forterres theory. However, it is not something I would talk about if i did not want to confuse my students....

Riveras and Lake coined the Ring of Life term, I believe, but their paper is not the one I'm thinking of. I was researching phylogenomics, and came across a number of papers trying to explain the three-way gene homology between the three domains, and most of them return an idea of lateral gene transfer being the explanation, with the conclusion that the root of the tree of life is not actually tree-like. I recall an excellent illustration with Darwin's original tree of life modified with arrows criss-crossing back and forth.

In any event, my use of the "Ring of Life" was just reaching into my brain for a descriptive term. I don't think Riveras and Lake's research was in any way conclusive - see the Bapteste and Walsh critique from 2005 - but I'd predict that phylogenomic research will continue to throw forth similar conclusions. I believe the paper I started with was this one: Phylogenomics and the Reconstruction of the Tree of Life, by Delsuc Brinkmann and Philippe, from which I bounced around through references and searches myself.

I'm just saying, positing that the viral RNA->DNA transition happened three times, explaining why there are three domains, seems pretty bizarre to me when phylogenetic analysis is revealing all sorts of questions regarding gene similar between all three domains. If the transition did happen three times for each domain, why are so many genes so closely similar between two domains? And if that's due to lateral gene transfer, then why posit that the transition happened three times in the first place, instead of just once?

@electricitylikesme: but wouldn't triplex DNA be even more resistant to enzymatic action? Also as a point of interest would the artificial DNA used in engineering require repair mechanisms to alleviate the molecular damage (free radicals et al) regular DNA needs to be checked for all the time?

What I'm basically saying is that a huge deal is being made over triplex DNA structures from this research but most of it seems basically motivated by the idea that 3 > 2 and therefore better somehow.

For engineering it's not particularly useful - the reason we're using DNA in the first place is because we need a reversible, programmable bond between nanoparticles - DNA is a good fit for this because all you do is attach a thiol group to the 3' end of two complementary strands and they'll stick to a pretty wide variety of metals (It's something like gold, silver and copper as well as a few others if you do some basic chemistry).

EDIT:
And it is as I thought (I've just been perusing the paper) - they do not report any interesting triplex like structures from artificial DNA strands containing an actual sequence of nucleotides (i.e. something like AATGCCCTAA).

Instead, what they find is that when you have a poly(A) and poly(T) strand (i.e. AAAAAAAAAAAAAAAAAAAA and the complementary TTTTTTTTTTTTTTTTTTTTTTT strand) then there is a strong tendency for a strand like this to permit insertion of a third poly(T) strand thanks to the way the molecules interact (they cite that it's probably from the symmetry of the molecule which means when the insertion takes place the various components interact favorably via Pi-Pi stacking, but I suppose we won't know for sure till someone kicks out an X-ray crystal structure - which would be really cool).

The relevant section of the paper, bold mine:

Homooligomers composed of A* and T* were subjected to hybridization experiments (entries 22−24 and Figure S9) and found to behave somewhat unlike the corresponding natural DNA does. The Job’s plot between d(A*)24 and d(T*)24 was conducted on the basis of UV−vis spectra at 0 °C after annealing processes (Figure 4b). Mole fraction of d(A*)24 was raised incrementally from 0% to 100% under conditions where the total concentration of d(A*)24 and d(T*)24 was maintained constant at 2.0 μM. In this experiment, we observed that one set of isosbestic points changed to the other set strictly when a mole fraction of d(A*)24 increased beyond 0.33. After that, the absorption bands of d(A*)24 simply grew in the spectra (Figure S10a). This behavior was also seen in the CD Job’s (Figure S10b) and titration (Figure S11) experiments. The thermal denaturation profiles revealed a similar two-state sigmoidal transition even when the molar ratio of d(A*)24 was varied (Figure 3c). Furthermore, the slope around the inflection point on the sigmoidal curve is much steeper than any other combination, indicating a strongly cooperative two-state transition (Figure S12). These data unambiguously suggest the exclusive formation of d(T*/A*/T*)24-type artificial triplex without d(A*/T*)24-type duplex even at the low concentration applied. This strong tendency for the formation of triplexes over duplexes should primarily be due to the symmetry of A* along the axis from the amino nitrogen to the carbon connected to the acetylene linker. Therefore, interaction of the third d(T*)24 strand with d(A*/T*)24 produces no energetic loss and rather adds a further stabilization arising from the enforced π-stacking interaction of the enlarged π-plane. This situation should cause the equilibrium constant between d(T*)24 and d(A*/T*)24 to be larger than that of the d(A*/T*)24 duplex formation, resulting in the observed two-state transition. In the cases of natural A and T homooligomers, the relative magnitudes of the two equilibrium constants are strongly depend on the concentrations of the oligomers and the existing salts.16 The selectivity for the formation of triplex over duplex is so high that the thermal denaturation study of the palindromic 20-mer in entry 25 displayed little hyperchromism and no apparent sigmoidal transition. This finding reconfirms that triplexes predominantly are formed rather than duplexes from the artificial DNAs composed only of A* and T*.